Dan Portik
@dportik.bsky.social
Bioinformatics scientist at PacBio. I currently work on metagenomics and methylation, but previously studied phylogenomics and frog/lizard evolution.
🦠 🐸 🦎 🧬
Free time: climbing 🧗, curling 🥌, and plants 🪴🌵.
🦠 🐸 🦎 🧬
Free time: climbing 🧗, curling 🥌, and plants 🪴🌵.
Here is an example from a lake water column microbiome, sequenced with #PacBio HiFi. In the HiFi-MAG-Pipeline, I look at reads mapped to all contigs, all bins (passing or failing QC), and only bins that pass QC (e.g., MAGs). The numbers vary by sample, but the overall pattern holds.
May 7, 2025 at 2:21 PM
Here is an example from a lake water column microbiome, sequenced with #PacBio HiFi. In the HiFi-MAG-Pipeline, I look at reads mapped to all contigs, all bins (passing or failing QC), and only bins that pass QC (e.g., MAGs). The numbers vary by sample, but the overall pattern holds.
Do you think long-read #metagenomics with #PacBio #HiFi is gaining momentum?
I noticed there were more publications & pre-prints on this topic in 2024 (56) than 2022 + 2023 combined (54).
Definitely encouraging, and I'm curious to see what 2025 brings!
Full pub list: github.com/PacificBiosc...
I noticed there were more publications & pre-prints on this topic in 2024 (56) than 2022 + 2023 combined (54).
Definitely encouraging, and I'm curious to see what 2025 brings!
Full pub list: github.com/PacificBiosc...
January 31, 2025 at 6:32 PM
Do you think long-read #metagenomics with #PacBio #HiFi is gaining momentum?
I noticed there were more publications & pre-prints on this topic in 2024 (56) than 2022 + 2023 combined (54).
Definitely encouraging, and I'm curious to see what 2025 brings!
Full pub list: github.com/PacificBiosc...
I noticed there were more publications & pre-prints on this topic in 2024 (56) than 2022 + 2023 combined (54).
Definitely encouraging, and I'm curious to see what 2025 brings!
Full pub list: github.com/PacificBiosc...
Great soil #metagenomics talk by @mikeschatz.bsky.social.
Few reads can be classified because everything is novel... so just build the reference catalogue first!
Hundreds of high-quality MAGs being recovered with #PacBio HiFi, and new sequencing with Vega is on par with quality from Revio.
Few reads can be classified because everything is novel... so just build the reference catalogue first!
Hundreds of high-quality MAGs being recovered with #PacBio HiFi, and new sequencing with Vega is on par with quality from Revio.
January 12, 2025 at 9:16 PM
Great soil #metagenomics talk by @mikeschatz.bsky.social.
Few reads can be classified because everything is novel... so just build the reference catalogue first!
Hundreds of high-quality MAGs being recovered with #PacBio HiFi, and new sequencing with Vega is on par with quality from Revio.
Few reads can be classified because everything is novel... so just build the reference catalogue first!
Hundreds of high-quality MAGs being recovered with #PacBio HiFi, and new sequencing with Vega is on par with quality from Revio.
Are you attending #PAG32? If so, stop by the #PacBio booth and see our new Vega benchtop sequencer!
Vega is quickly becoming a top choice for microbial applications, including isolate sequencing, full-length #16S, and #metagenomics.
Vega is quickly becoming a top choice for microbial applications, including isolate sequencing, full-length #16S, and #metagenomics.
January 12, 2025 at 8:29 PM
Are you attending #PAG32? If so, stop by the #PacBio booth and see our new Vega benchtop sequencer!
Vega is quickly becoming a top choice for microbial applications, including isolate sequencing, full-length #16S, and #metagenomics.
Vega is quickly becoming a top choice for microbial applications, including isolate sequencing, full-length #16S, and #metagenomics.
Another very insightful paper on #methylation and long-read sequencing by @gangfang.bsky.social, describing some important but frequently overlooked caveats.
Gang provides a fantastic summary in his post, but here's my take too😅:
Gang provides a fantastic summary in his post, but here's my take too😅:
November 20, 2024 at 7:25 PM
Another very insightful paper on #methylation and long-read sequencing by @gangfang.bsky.social, describing some important but frequently overlooked caveats.
Gang provides a fantastic summary in his post, but here's my take too😅:
Gang provides a fantastic summary in his post, but here's my take too😅:
It's beautiful weather today at the #cshlmbiome conference!
#PacBio just hosted a packed microbial workshop featuring guest speaker Gang Fang. He talked about studying the stable and dynamic nature of bacterial epigenomes, with an emphasis on HiFi #methylation data.
#PacBio just hosted a packed microbial workshop featuring guest speaker Gang Fang. He talked about studying the stable and dynamic nature of bacterial epigenomes, with an emphasis on HiFi #methylation data.
October 31, 2024 at 7:21 PM
It's beautiful weather today at the #cshlmbiome conference!
#PacBio just hosted a packed microbial workshop featuring guest speaker Gang Fang. He talked about studying the stable and dynamic nature of bacterial epigenomes, with an emphasis on HiFi #methylation data.
#PacBio just hosted a packed microbial workshop featuring guest speaker Gang Fang. He talked about studying the stable and dynamic nature of bacterial epigenomes, with an emphasis on HiFi #methylation data.
Don't miss out on this free #metagenomics webinar next week!
PacBio HiFi sequencing on Revio can be used to generate single-contig, complete MAGs from the most difficult sample type to assemble - soil.
Results for wetland and grassland soil shown here, from my talk at LAMG.
bit.ly/3Tf9qJj
PacBio HiFi sequencing on Revio can be used to generate single-contig, complete MAGs from the most difficult sample type to assemble - soil.
Results for wetland and grassland soil shown here, from my talk at LAMG.
bit.ly/3Tf9qJj
September 24, 2024 at 5:12 PM
Don't miss out on this free #metagenomics webinar next week!
PacBio HiFi sequencing on Revio can be used to generate single-contig, complete MAGs from the most difficult sample type to assemble - soil.
Results for wetland and grassland soil shown here, from my talk at LAMG.
bit.ly/3Tf9qJj
PacBio HiFi sequencing on Revio can be used to generate single-contig, complete MAGs from the most difficult sample type to assemble - soil.
Results for wetland and grassland soil shown here, from my talk at LAMG.
bit.ly/3Tf9qJj
I also introduced a new tool called pb-MAG-mirror, which allows detailed comparisons of two MAG sets.
MAGs are assigned to the categories here, showing where the two binning methods agree and disagree.
It also performs dereplication and merging based on these categories.
3/6
MAGs are assigned to the categories here, showing where the two binning methods agree and disagree.
It also performs dereplication and merging based on these categories.
3/6
May 13, 2024 at 6:56 PM
I also introduced a new tool called pb-MAG-mirror, which allows detailed comparisons of two MAG sets.
MAGs are assigned to the categories here, showing where the two binning methods agree and disagree.
It also performs dereplication and merging based on these categories.
3/6
MAGs are assigned to the categories here, showing where the two binning methods agree and disagree.
It also performs dereplication and merging based on these categories.
3/6
We used all the latest tools for HiFi #metagenomics, serving as a tutorial and comparison.
Assembly was performed with hifiasm-meta and metaMDBG.
Binning included the HiFi-MAG-Pipeline and proximity ligation (Hi-C) methods from
@phasegenomics.bsky.social
2/6
Assembly was performed with hifiasm-meta and metaMDBG.
Binning included the HiFi-MAG-Pipeline and proximity ligation (Hi-C) methods from
@phasegenomics.bsky.social
2/6
May 13, 2024 at 6:55 PM
We used all the latest tools for HiFi #metagenomics, serving as a tutorial and comparison.
Assembly was performed with hifiasm-meta and metaMDBG.
Binning included the HiFi-MAG-Pipeline and proximity ligation (Hi-C) methods from
@phasegenomics.bsky.social
2/6
Assembly was performed with hifiasm-meta and metaMDBG.
Binning included the HiFi-MAG-Pipeline and proximity ligation (Hi-C) methods from
@phasegenomics.bsky.social
2/6
Thoroughly enjoyed this special gift from
Zymo Research!
It's not in their product catalogue, but if you're lucky you might find it at a research conference or an in-person meeting 🍻 😉
Zymo Research!
It's not in their product catalogue, but if you're lucky you might find it at a research conference or an in-person meeting 🍻 😉
October 6, 2023 at 5:51 PM
Thoroughly enjoyed this special gift from
Zymo Research!
It's not in their product catalogue, but if you're lucky you might find it at a research conference or an in-person meeting 🍻 😉
Zymo Research!
It's not in their product catalogue, but if you're lucky you might find it at a research conference or an in-person meeting 🍻 😉